csd3
The system
1. System
2. Login
3. Directories
4. Policies
5. email
6. Software
7. ceuadmin
8. Parallel Computing
9. Green Algorithms
10. Training
11. Contacts
12. Acknowledgement
/systems/files/
The CEU software repository at CSD3
cardio
Applications
1. ABCtoolbox
2. AEGIS
3. akt
4. ANNOVAR
5. aria2
6. bcftools
7. bedops
8. bgenix
9. CaVEMaN
10. CAVIAR/eCAVIAR
11. circos
12. citeproc
13. CookHLA
14. Cytoscape
15. DNAnexus
16. DosageConverter
17. finemap
18. GATK
19. GCTA
20. Genotype-Harmonizer
21. gsutil
22. hail
23. HESS
24. KentUtils
25. lapack
26. LEMMA
27. LocusZoom
28. METAL
29. MetaXcan
30. pandoc
31. PCA projection
32. PLINK
33. polyphen-2
34. poppler
35. PRSice
36. PRSoS
37. pspp
38. AlphaPept and PyOpenMS
39. qpdf
40. qtltools
41. quarto
42. regenie
43. R
44. RStudio
45. shapeit
46. SMR
47. snipar
48. SNPTEST
49. sra-tools
50. SurvivalGWAS_SV
51. tabix
52. VEP
53. Visual Studio code
/applications/files/
/applications/files/examples/
Python packages
1. gwas2vcf
2. GWAS Catalog
3. ldsc
4. PhySO
5. snakemake
6. Synapse
R packages
1. brms
2. conquer
3. EasyQC
4. geometries
5. glmnet
6. gnn
7. gsl
8. jqr
9. LDlinkR
10. magick
11. METRO
12. nloptr
13. PhenoScanner
14. PKI
15. plumber
16. protolite
17. RcppTOML
18. Rfast
19. rgdal
20. rgeos
21. rgl
22. Rhdf5lib
23. rjags
24. rJava
25. rstan
26. SAIGE
27. sf
28. snpnet
29. sojo
30. SPACox
31. tenXplore
32. xlsx
csd3
systems
policies.md
Policies
See
https://docs.hpc.cam.ac.uk/hpc/user-guide/policies.html#acknowledging-csd3
.
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2019-2023,
cambridge-ceu
Revision
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